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This paper presents a comprehensive analysis of a novel temporal dataset of Shewanella oneidensis. Here we propose to cluster the temporal gene expression data of Shewanella oneidensis to define its molecular response at different time intervals following acidic pH and basic pH exposure and to find a relation of these temporal data at different environmental conditions. A mapping between those clusters is also defined to describe the interaction and reaction of those genes in different time in two separate conditions. Several conceptually variant clustering algorithms are applied to find the actual structure within data and the results of clustering algorithms are evaluated by several robust internal indices.